Mercurial > repos > bgruening > openbabel
comparison visualisation/ob_depiction_svg.xml @ 2:125da3a296ca draft default tip
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author | bgruening |
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date | Wed, 15 Jul 2015 12:13:08 -0400 |
parents | 527ecd2fc500 |
children |
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1:b52872a1755a | 2:125da3a296ca |
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2 <description>of compounds</description> | 2 <description>of compounds</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="2.3.2">openbabel</requirement> | 4 <requirement type="package" version="2.3.2">openbabel</requirement> |
5 </requirements> | 5 </requirements> |
6 <command> | 6 <command> |
7 <![CDATA[ | |
7 obabel -i${infile.ext} $infile | 8 obabel -i${infile.ext} $infile |
8 $embed_molecule_as_cml | 9 $embed_molecule_as_cml |
9 $draw_all_carbon_atoms | 10 $draw_all_carbon_atoms |
10 -xC | 11 -xC |
11 -O | 12 -O |
12 $outfile -o$oformat | 13 $outfile -o$oformat |
13 #if str($sort) != "none": | 14 #if str($sort) != "none": |
14 --sort $sort | 15 --sort $sort |
15 #end if | 16 #end if |
16 #if str($display_name) != "None" and len(str($display_name)) > 0 and str($display_name) != 'title': | 17 #if str($display_name) != "None" and len(str($display_name)) > 0 and str($display_name) != 'title': |
17 --append "$display_name" | 18 --append "$display_name" |
18 --title "" | 19 --title "" |
19 #end if | 20 #end if |
20 $thick_lines | 21 $thick_lines |
21 2>&1 | 22 2>&1 |
23 ]]> | |
22 </command> | 24 </command> |
23 <inputs> | 25 <inputs> |
24 <param name="infile" type="data" format="mol,sdf,smi,inchi" label="Input format"/> | 26 <param name="infile" type="data" format="mol,sdf,smi,inchi" label="Input format"/> |
25 <param name="embed_molecule_as_cml" type="boolean" truevalue="-e" falsevalue="" label="Embed molecule as CML"/> | 27 <param name="embed_molecule_as_cml" type="boolean" truevalue="-e" falsevalue="" label="Embed molecule as CML"/> |
26 <param name="draw_all_carbon_atoms" type="boolean" truevalue="-a" falsevalue="" label="draw all carbon atoms"/> | 28 <param name="draw_all_carbon_atoms" type="boolean" truevalue="-a" falsevalue="" label="draw all carbon atoms"/> |
93 <param name='sort' value='none' /> | 95 <param name='sort' value='none' /> |
94 <output name="outfile" ftype="svg" file="ob_depiction_svg_on_8_mol.svg" /> | 96 <output name="outfile" ftype="svg" file="ob_depiction_svg_on_8_mol.svg" /> |
95 </test> | 97 </test> |
96 </tests> | 98 </tests> |
97 <help> | 99 <help> |
100 <![CDATA[ | |
98 | 101 |
99 .. class:: infomark | 102 .. class:: infomark |
100 | 103 |
101 **What this tool does** | 104 **What this tool does** |
102 | 105 |
121 | 124 |
122 `Open Babel`_ | 125 `Open Babel`_ |
123 | 126 |
124 .. _Open Babel: http://openbabel.org/wiki/Main_Page | 127 .. _Open Babel: http://openbabel.org/wiki/Main_Page |
125 | 128 |
129 ]]> | |
126 </help> | 130 </help> |
127 </tool> | 131 </tool> |